全外显子测序联合基因组拷贝数变异测序在儿科遗传病诊断中的应用

doi:10.3760/cma.j.issn.1007-1245.2024.04.001

摘要/Abstract

摘要：

目的　探讨全外显子测序（whole exome sequencing，WES）联合基因组拷贝数变异测序（copy number variation sequencing，CNVseq）在儿科遗传病诊断中的应用价值。方法　选取2019年8月至2023年7月郑州市妇幼保健院新生儿科及儿科收治的怀疑患有遗传性疾病或临床诊断不明确的患儿为研究对象，采集患儿及其父母外周血进行WES及CNVseq检测，对检出的变异进行分类及评级，并进行一代测序或qPCR验证。结果　共纳入患儿33例，其中男性18例，女性15例，年龄范围为1 d～8岁。WES的阳性检出率为36.4%（12/33），CNVseq阳性检出率为9.1%（3/33），两者联合阳性检出率为45.5%（15/33）。结论　WES联合CNVseq是儿童遗传性疾病分子诊断的有力工具，可作为一线检测手段在临床大力推广。

关键词:

全外显子测序, 基因组拷贝数变异测序, 遗传病, 检出率, 儿童

Abstract:

Objective　To explore the significance of whole exome sequencing (WES) accompanied by copy number variation sequencing (CNVseq) in the diagnosis of pediatric genetic diseases. Methods　Children with suspected genetic diseases or unclear clinical diagnosis admitted to the departments of neonatology and pediatrics of Women & Infants Hospital of Zhengzhou from August 2019 to July 2023 were selected as the study objects. The peripheral blood of the children and their parents were collected for WES and CNVseq. The detected genetic mutations were classified according to American College of Medical Genetics and Genomics (ACMG) classification, and Sanger sequencing or qPCR was performed to verify the mutations. Results　A total of 33 children were enrolled, including 18 boys and 15 girls, aged 1 d to 8 years. The positive detection rate of WES was 36.4% (12/33), the positive detection rate of CNVseq was 9.1% (3/33), and the positive detection rate of the combination of WES and CNVseq was 45.5% (15/33). Conclusion　WES accompanied by CNVseq is a powerful tool for molecular diagnosis of pediatric genetic diseases and can be widely used as a first-line detection method in clinical practice.

Key words:

Whole exome sequencing, Copy number variation sequencing, Genetic diseases, Diagnostic rate, Children

张华刘敏袁路杨黎明张富青.

全外显子测序联合基因组拷贝数变异测序在儿科遗传病诊断中的应用 [J]. 国际医药卫生导报, 2024, 30(4): 529-534.

Zhang Hua, Liu Min, Yuan Lu, Yang Liming, Zhang Fuqing.

Application of WES accompanied by CNVseq in the diagnosis of pediatric genetic diseases [J]. International Medicine and Health Guidance News, 2024, 30(4): 529-534.

参考文献

[1] Borghesi A, Mencarelli MA, Memo L, et al. Intersociety policy statement on the use of whole-exome sequencing in the critically ill newborn infant[J]. Ital J Pediatr, 2017, 43(1):100. DOI: 10.1186/s13052-017-0418-0.
[2] 王慧君,周文浩.精准医疗时代新生儿遗传病临床干预面临的机遇与挑战[J].中华儿科杂志,2018,56(4):244-246. DOI:10.3760/cma.j.issn.0578-1310.2018.04.002.
[3] Nazeha N, Koh AL, Kam S, et al. Reduced resource utilization with early use of next-generation sequencing in rare genetic diseases in an Asian cohort[J]. Am J Med Genet A, 2022, 188(12):3482-3491. DOI: 10.1002/ajmg.a.62974.
[4] Wheeler DA, Srinivasan M, Egholm M, et al. The complete genome of an individual by massively parallel DNA sequencing[J]. Nature, 2008, 452(7189):872-876. DOI: 10.1038/nature06884.
[5] Marshall DA, Benchimol EI, MacKenzie A, et al. Direct health-care costs for children diagnosed with genetic diseases are significantly higher than for children with other chronic diseases[J]. Genet Med, 2019, 21(5):1049-1057. DOI: 10.1038/s41436-018-0289-9.
[6] Richards S, Aziz N, Bale S, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology[J]. Genet Med, 2015, 17(5):405-424. DOI: 10.1038/gim.2015.30.
[7] Arth AC, Tinker SC, Simeone RM, et al. Inpatient hospitalization costs associated with birth defects among persons of all ages - United States, 2013[J]. MMWR Morb Mortal Wkly Rep, 2017, 66(2):41-46. DOI: 10.15585/mmwr.mm6602a1.
[8] Moffitt KB, Case AP, Farag NH, et al. Hospitalization charges for children with birth defects in Texas, 2001 to 2010[J]. Birth Defects Res A Clin Mol Teratol, 2016, 106(3):155-163. DOI: 10.1002/bdra.23470.
[9] Gonzaludo N, Belmont JW, Gainullin VG, et al. Estimating the burden and economic impact of pediatric genetic disease[J]. Genet Med, 2019, 21(8):1781-1789. DOI: 10.1038/s41436-018-0398-5.
[10] 高晓鹏,杨颖.6285例遗传咨询儿童外周血染色体核型分析[J].中国优生与遗传杂志,2022,30(4):645-649. DOI:10.13404/j.cnki.cjbhh.20220324.002.
[11] 刘为,涂明,赵溜,等.3142例遗传咨询儿童外周血染色体核型分析[J].实用检验医师杂志,2022,14(4):428-431. DOI:10.3969/j.issn.1674-7151.2022.04.023.
[12] 田海英,罗真真,汪琳琳,等.染色体微阵列技术在产科和儿科遗传病诊断中的临床应用价值分析[J].国际检验医学杂志,2022,43(6):701-704. DOI:10.3969/j.issn.1673-4130. 2022.06.014.
[13] Lee JY, Oh SH, Keum C, et al. Clinical application of prospective whole-exome sequencing in the diagnosis of genetic disease: experience of a regional disease center in South Korea[J]. Ann Hum Genet, 2023. DOI: 10.1111/ahg.12530.
[14] Trujillano D, Bertoli-Avella AM, Kumar Kandaswamy K, et al. Clinical exome sequencing: results from 2819 samples reflecting 1000 families[J]. Eur J Hum Genet, 2017, 25(2):176-182. DOI: 10.1038/ejhg.2016.146.
[15] 齐志业,段江,贺湘英,等.全外显子组测序在危重症新生儿单基因遗传病中的临床应用[J].中国当代儿科杂志,2019,21(7):640-643. DOI:10.7499/j.issn.1008-8830.2019. 07.005.
[16] Nair P, Sabbagh S, Mansour H, et al. Contribution of next generation sequencing in pediatric practice in Lebanon. A study on 213 cases[J]. Mol Genet Genomic Med, 2018, 6(6):1041-1052. DOI: 10.1002/mgg3.480.
[17] Retterer K, Juusola J, Cho MT, et al. Clinical application of whole-exome sequencing across clinical indications[J]. Genet Med, 2016, 18(7):696-704. DOI: 10.1038/gim.2015.148.
[18] Zhu X, Petrovski S, Xie P, et al. Whole-exome sequencing in undiagnosed genetic diseases: interpreting 119 trios[J]. Genet Med, 2015, 17(10):774-781. DOI: 10.1038/gim.2014.191.
[19] Yang Y, Muzny DM, Xia F, et al. Molecular findings among patients referred for clinical whole-exome sequencing[J]. JAMA, 2014, 312(18):1870-1879. DOI: 10.1001/jama.2014.14601.
[20] Posey JE, Rosenfeld JA, James RA, et al. Molecular diagnostic experience of whole-exome sequencing in adult patients[J]. Genet Med, 2016, 18(7):678-685. DOI: 10.1038/gim.2015.142.
[21] Alfares A, Alfadhel M, Wani T, et al. A multicenter clinical exome study in unselected cohorts from a consanguineous population of Saudi Arabia demonstrated a high diagnostic yield[J]. Mol Genet Metab, 2017, 121(2):91-95. DOI: 10.1016/j.ymgme.2017.04.002.
[22] Al-Shamsi A, Hertecant JL, Souid AK, et al. Whole exome sequencing diagnosis of inborn errors of metabolism and other disorders in United Arab Emirates[J]. Orphanet J Rare Dis, 2016, 11(1):94. DOI: 10.1186/s13023-016- 0474-3.
[23] Redon R, Ishikawa S, Fitch KR, et al. Global variation in copy number in the human genome[J]. Nature, 2006, 444(7118):444-454. DOI: 10.1038/nature05329.
[24] Alibutud R, Hansali S, Cao X, et al. Structural variations contribute to the genetic etiology of autism spectrum disorder and language impairments[J]. Int J Mol Sci, 2023, 24(17):13248. DOI: 10.3390/ijms241713248.
[25] Montanucci L, Lewis-Smith D, Collins RL, et al. Genome-wide identification and phenotypic characterization of seizure-associated copy number variations in 741,075 individuals[J]. Nat Commun, 2023, 14(1):4392. DOI: 10.1038/s41467-023-39539-6.
[26] Wang H, Dombroski BA, Cheng PL, et al. Structural variation detection and association analysis of whole-genome-sequence data from 16,905 Alzheimer's diseases sequencing project subjects. medRxiv [Preprint]. 2023 Sep 13:2023.09.13.23295505. DOI: 10.1101/2023.09.13.23295505.
[27] Jagannath V, Grünblatt E, Theodoridou A, et al. Rare copy number variants in individuals at clinical high risk for psychosis: enrichment of synaptic/brain-related functional pathways[J]. Am J Med Genet B Neuropsychiatr Genet, 2020, 183(2):140-151. DOI: 10.1002/ajmg.b.32770.
[28] Larroya M, Tortajada M, Mensión E, et al. Have maternal or paternal ages any impact on the prenatal incidence of genomic copy number variants associated with fetal structural anomalies?[J]. PLoS One, 2021, 16(7):e0253866. DOI: 10.1371/journal.pone.0253866.
[29] Ewans LJ, Schofield D, Shrestha R, et al. Whole-exome sequencing reanalysis at 12 months boosts diagnosis and is cost-effective when applied early in Mendelian disorders[J]. Genet Med, 2018, 20(12):1564-1574. DOI: 10.1038/gim.2018.39.
[30] Jalkh N, Corbani S, Haidar Z, et al. The added value of WES reanalysis in the field of genetic diagnosis: lessons learned from 200 exomes in the Lebanese population[J]. BMC Med Genomics, 2019, 12(1):11. DOI: 10.1186/s12920-019-0474-y.